Thank you, that fixed it. I'm configuring it now; liking it as I test it out, but running into some questions:
1. It won't accept "-Z Axis" or any non-numerical value as the input for firing a weapon -- I suspect I would not be alone among many players in thinking the right-hand trigger button on a standard "Xbox for Windows" controller is the appropriate place for the "fire weapons" input.
2. There doesn't seem to be a strafing axis or any kind of input -- am I just missing it? It seems impossible to strafe at all with the controller, even though there's a perfectly good X Axis .
3. Y Axis inversion for Acceleration seems to do nothing. Pulling down on the left stick, which is to say providing a negative Y axis input, regardless of whether the Acceleration Inversion setting is true or false, always provides forward acceleration to the ship, when the Y Axis is used as the Acceleration input.
My feedback is that in general it's pretty good, I just wish I could strafe (or "sideways accelerate") on the X Axis and use a non-inverted Y Axis for forward/backward acceleration. There are a few button-only options I wish I could map to axes. It might be a good idea to pre-map for the most common controller layouts (Xbox for Windows, and DualShock... if there is a USB Dualshock???) and let users just pick from those configurations, as otherwise there's a bit of a steep learning curve. Once I get a mapping worked out that makes sense to me, I'll post it here along with a basic guide to get the mod working and setting it up, for anyone else that might benefit. But without being able to figure out a way to strafe, de-invert the Y axis for acceleration, and fire on the Z axis I'm going to keep using the keyboard for the moment.
I think I recall seeing a thread a long time ago where people responded to the idea of controller support with a mixture of disgust/anger/fear/heresy/etc. and I have to say, actually it works really well, and it's clear a lot of work went in under the hood here to get things to work (AI control of omni-shield direction is nice). Phase 2 design would include controls for the battle map, Phase 3 for the campaign, but controlling an individual ship actually feels quite nice, with the above caveats.